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Approaches to the calculation of the full state vector of a larger epidemiological model for the spread of COVID-19 in Sweden at the initial time instant from available data and with a simplified dynamical model are proposed and evaluated. The larger epidemiological model is based on a continuous Markov chain and captures the demographic composition of and the transport flows between the counties of Sweden. Its intended use is to predict the outbreak development in temporal and spatial coordinates as well as across the demographic groups. It can also support evaluating and comparing of prospective intervention strategies in terms of e.g. lockdown in certain areas or isolation of specific age groups. The simplified model is a discrete time-invariant linear system that has cumulative infectious incidence, infected population, asymptomatic population, exposed population, and infectious pressure as the state variables. Since the system matrix of the model depends on a number transition rates, structural properties of the model are investigated for suitable parameter ranges. It is concluded that the model becomes unobservable for some parameter values. Two contrasting approaches to the initial state estimation are considered. One is a version of Rauch-Tung-Striebel smoother and another is based on solving a batch nonlinear optimization problem. The benefits and shortcomings of the considered estimation techniques are analyzed and compared on synthetic data for several Swedish counties., Comment: 7 pages, 8 figures

BackgroundThe response of the Swedish authorities to the COVID-19 pandemic was less restrictive than in most countries during the first year, with infection and death rates substantially higher than in neighbouring Nordic countries. Because access to PCR testing was limited during the first wave (February to June 2020) and regional data were reported with delay, adequate monitoring of community disease spread was hampered. The app-based COVID Symptom Study was launched in Sweden to disseminate real-time estimates of disease spread and to collect prospective data for research. The aim of this study was to describe the research project, develop models for estimation of COVID-19 prevalence and to evaluate it for prediction of hospital admissions for COVID-19. MethodsWe enrolled 143 531 study participants ([≥]18 years) throughout Sweden, who contributed 10{middle dot}6 million daily symptom reports between April 29, 2020 and February 10, 2021. Data from 19 161 self-reported PCR tests were used to create a symptom-based algorithm to estimate daily prevalence of symptomatic COVID-19. The prediction model was validated using external datasets. We further utilized the model estimates to forecast subsequent new hospital admissions. FindingsA prediction model for symptomatic COVID-19 based on 17 symptoms, age, and sex yielded an area under the ROC curve of 0{middle dot}78 (95% CI 0{middle dot}74-0{middle dot}83) in an external validation dataset of 943 PCR-tested symptomatic individuals. App-based surveillance proved particularly useful for predicting hospital trends in times of insufficient testing capacity and registration delays. During the first wave, our prediction model estimates demonstrated a lower mean error (0{middle dot}38 average new daily hospitalizations per 100 000 inhabitants per week (95% CI 0{middle dot}32, 0{middle dot}45)) for subsequent hospitalizations in the ten most populated counties, than a model based on confirmed case data (0{middle dot}72 (0{middle dot}64, 0{middle dot}81)). The model further correctly identified on average three out of five counties (95% CI 2{middle dot}3, 3{middle dot}7) with the highest rates of hospitalizations the following week during the first wave and four out of five (3{middle dot}0, 4{middle dot}6) during the second wave. InterpretationThe experience of the COVID Symptom Study highlights the important role citizens can play in real-time monitoring of infectious diseases, and how app-based data collection may be used for data-driven rapid responses to public health challenges. FundingSwedish Heart-Lung Foundation (20190470, 20140776), Swedish Research Council (EXODIAB, 2009-1039; 2014-03529), European Commission (ERC-2015-CoG - 681742 NASCENT), and Swedish Foundation for Strategic Research (LUDC-IRC, 15-0067) to MG or PF. European Research Council Starting Grant (801965) to TF. NO was financially supported by the Knut and Alice Wallenberg Foundation as part of the National Bioinformatics Infrastructure Sweden at SciLifeLab. ATC was supported in this work through the Massachusetts Consortium on Pathogen Readiness (MassCPR). ZOE Limited provided in-kind support for all aspects of building, running and supporting the app and service to all users worldwide. Support for this study for KCL researchers was provided by the National Institute for Health Research (NIHR)-funded Biomedical Research Centre based at Guys and St Thomas (GSTT) NHS Foundation Trust. This work was supported by the UK Research and Innovation London Medical Imaging & Artificial Intelligence Centre for Value-Based Healthcare. Investigators also received support from the Wellcome Trust, Medical Research Council (MRC), British Heart Foundation (BHF), Alzheimers Society, European Union, NIHR, COVID-19 Driver Relief Fund (CDRF) and the NIHR-funded BioResource, Clinical Research Facility and Biomedical Research Centre (BRC) based at GSTT NHS Foundation Trust in partnership with KCL. ZOE Limited developed the app for data collection as a not-for-profit endeavour. None of the funding entities had any role in study design, data analysis, data interpretation, or the writing of this manuscript.

We develop an efficient and high order panel method with applications in airfoil design. Through the use of analytic work and careful considerations near singularities our approach is quadrature-free. The resulting method is examined with respect to accuracy and efficiency and we discuss the different trade-offs in approximation order and computational complexity. A reference implementation within a package for a two-dimensional fast multipole method is distributed freely.

Neuronal models based on the Hodgkin-Huxley equation form a fundamental framework in the field of computational neuroscience. While the neuronal state is often modeled deterministically, experimental recordings show stochastic fluctuations, presumably driven by molecular noise from the underlying microphysical conditions. In turn, the firing of individual neurons gives rise to an electric field n extracellular space, also thought to affect the firing pattern of nearby neurons. We develop a multiscale model which combines a stochastic ion channel gating process taking place on the neuronal membrane, together with the propagation of an action potential along the neuronal structure. We also devise a numerical method relying on a split-step strategy which effectively couples these two processes and we experimentally test the feasibility of this approach. We finally also explain how the approach can be extended with Maxwell's equations to allow the potential to be propagated in extracellular space., 23 pages, 10 figures

Mathematical epidemiological models have a broad use, including both qualitative and quantitative applications. With the increasing availability of data, large-scale quantitative disease spread models can nowadays be formulated. Such models have a great potential, e.g., in risk assessments in public health. Their main challenge is model parameterization given surveillance data, a problem which often limits their practical usage. We offer a solution to this problem by developing a Bayesian methodology suitable to epidemiological models driven by network data. The greatest difficulty in obtaining a concentrated parameter posterior is the quality of surveillance data; disease measurements are often scarce and carry little information about the parameters. The often overlooked problem of the model's identifiability therefore needs to be addressed, and we do so using a hierarchy of increasingly realistic known truth experiments. Our proposed Bayesian approach performs convincingly across all our synthetic tests. From pathogen measurements of shiga toxin-producing Escherichia coli O157 in Swedish cattle, we are able to produce an accurate statistical model of first-principles confronted with data. Within this model we explore the potential of a Bayesian public health framework by assessing the efficiency of disease detection and -intervention scenarios. eSSENCE

We present the R package SimInf which provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simulation algorithm and incorporates available data such as births, deaths and movements as scheduled events at predefined time-points. Using C code for the numerical solvers and OpenMP to divide work over multiple processors ensures high performance when simulating a sample outcome. One of our design goal was to make SimInf extendable and enable usage of the numerical solvers from other R extension packages in order to facilitate complex epidemiological research. In this paper, we provide a technical description of the framework and demonstrate its use on some basic examples. We also discuss how to specify and extend the framework with user-defined models., The manual has been updated to the latest version of SimInf (v6.0.0). 41 pages, 16 figures